LAMMPS (17 Apr 2024)
# three orthogonal periodic CNTs
# demo for replicating triply looped system
# infinite loops in x, y, z
# includes bonded interactions across box corners
# includes bonds, angles, dihedrals, impropers (class2)

units real

boundary p p p

atom_style full

pair_style lj/class2 10

angle_style class2

bond_style class2

dihedral_style class2

improper_style class2

read_data three_periodic_CNTs.data.gz
Reading data file ...
  orthogonal box = (0 0 0) to (80.96 80.96 80.96)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  3168 atoms
  reading velocities ...
  3168 velocities
  scanning bonds ...
  3 = max bonds/atom
  scanning angles ...
  3 = max angles/atom
  scanning dihedrals ...
  12 = max dihedrals/atom
  scanning impropers ...
  1 = max impropers/atom
  orthogonal box = (0 0 0) to (80.96 80.96 80.96)
  1 by 1 by 1 MPI processor grid
  reading bonds ...
  4752 bonds
  reading angles ...
  9504 angles
  reading dihedrals ...
  19008 dihedrals
  reading impropers ...
  3168 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     3 = max # of 1-2 neighbors
     6 = max # of 1-3 neighbors
    18 = max # of 1-4 neighbors
    18 = max # of special neighbors
  special bonds CPU = 0.002 seconds
  read_data CPU = 0.056 seconds

replicate 2 2 2 bond/periodic
Replication is creating a 2x2x2 = 8 times larger system...
  orthogonal box = (0 0 0) to (161.92 161.92 161.92)
  1 by 1 by 1 MPI processor grid
  bounding box image = (0 0 0) to (0 0 0)
  bounding box extra memory = 1.62 MB
  average # of replicas added to proc = 8.00 out of 8 (100.00%)
  25344 atoms
  38016 bonds
  76032 angles
  152064 dihedrals
  25344 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     3 = max # of 1-2 neighbors
     6 = max # of 1-3 neighbors
    18 = max # of 1-4 neighbors
    18 = max # of special neighbors
  special bonds CPU = 0.012 seconds
  replicate CPU = 0.027 seconds

fix 1 all nve

run 100
Generated 0 of 0 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 27 27 27
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/class2, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
WARNING: Inconsistent image flags (../domain.cpp:1051)
Per MPI rank memory allocation (min/avg/max) = 51.87 | 51.87 | 51.87 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0             -14266.189      1466925.5      1452659.3     -29908.753    
       100   2155.9128     -17224.188      1306769.8      1452409        1985.2082    
Loop time of 5.0155 on 1 procs for 100 steps with 25344 atoms

Performance: 1.723 ns/day, 13.932 hours/ns, 19.938 timesteps/s, 505.314 katom-step/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.6557     | 1.6557     | 1.6557     |   0.0 | 33.01
Bond    | 3.2813     | 3.2813     | 3.2813     |   0.0 | 65.42
Neigh   | 0.047025   | 0.047025   | 0.047025   |   0.0 |  0.94
Comm    | 0.0085317  | 0.0085317  | 0.0085317  |   0.0 |  0.17
Output  | 7.8551e-05 | 7.8551e-05 | 7.8551e-05 |   0.0 |  0.00
Modify  | 0.014635   | 0.014635   | 0.014635   |   0.0 |  0.29
Other   |            | 0.008159   |            |       |  0.16

Nlocal:          25344 ave       25344 max       25344 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          22737 ave       22737 max       22737 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    2.89358e+06 ave 2.89358e+06 max 2.89358e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 2893576
Ave neighs/atom = 114.17203
Ave special neighs/atom = 18
Neighbor list builds = 1
Dangerous builds = 0

# write_restart replicate.restart
# write_data replicate.data
Total wall time: 0:00:05
